Recently another unnatural base pair d5SICS-dNaM has been reported to be self replicating ( Nature 509, 385–388 (15 May 2014)). The crystal structure of the pair has been solved (PDB code 4C8K to 4C8O) but the most problematic thing I have noticed that the DNA chain is breaking when the pair (d5SICS-dNaM) comes. I'm still wondering how the pair be stable and orient inside the unbroken DNA chain as the pairs are relatively bigger than the natural base pairs. I have done some DFT calculation which clearly showing possible breaking of hydrogen-bonds of neighboring natural base pairs due to the presence of this unnatural base pair. Experts please show light on the issue.
http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html
http://www.rcsb.org/pdb/explore/explore.do?structureId=4C8K